Harada was after Logan. The Yakuza were after Mariko. There were two hits going on at the same time. Viper tells Harada later that he she needed him "to bring her the mutant", and that she had poisoned him to make him easier for him to capture, and that he had failed her for not doing so.

Yashida didn't fake his death, exactly. His death was imminent. The armor was the only thing that could keep him alive and they were getting him to the armor as quickly as possible, but leading everyone else to believe that he had died. He would have actually died if they hadn't moved him.

Since there was already a plan to assassinate Mariko, they set it up so it would look like Logan was just another victim at the funeral shootout. It wasn't enough that Logan had been poisoned, he needed to be injured badly enough for them to take as well. Presuming it couldn't have been done in the Yashida house, that was the plan to injure him and take him.

The "power squabble" in the family was already there. It was caused by Yashida's obsession, and had gone on for years prior to Logan ever arriving in Tokyo.